Origins and evolution of modern biochemistry: insights from genomes and molecular structure

Caetano‐Anollés, Gustavo; Sun, Feng; Wang, Minglei; Yafremava, Liudmila S.; Harish, Ajith; Kim, Hee Shin; Knudsen, Vegeir; Caetano-Anollés, Derek; Mittenthal, Jay E.

doi:10.2741/3077

Cited by 17 publications

(13 citation statements)

References 240 publications

(284 reference statements)

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“…Evolution's arrow is established directly by the evolutionary model, the rationale and assumptions of which have been recently reviewed [51]. Operationally, the tree reconstruction algorithm finds the shortest unrooted tree(s) without specifying character polarity and then roots the tree(s) by invoking a hypothetical ancestor defined by ancestral character states and selecting the rooted topology that minimizes overall tree length (see Methods).…”

Section: Discussionmentioning

confidence: 99%

The proteomic complexity and rise of the primordial ancestor of diversified life

2011

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BackgroundThe last universal common ancestor represents the primordial cellular organism from which diversified life was derived. This urancestor accumulated genetic information before the rise of organismal lineages and is considered to be either a simple 'progenote' organism with a rudimentary translational apparatus or a more complex 'cenancestor' with almost all essential biological processes. Recent comparative genomic studies support the latter model and propose that the urancestor was similar to modern organisms in terms of gene content. However, most of these studies were based on molecular sequences, which are fast evolving and of limited value for deep evolutionary explorations.ResultsHere we engage in a phylogenomic study of protein domain structure in the proteomes of 420 free-living fully sequenced organisms. Domains were defined at the highly conserved fold superfamily (FSF) level of structural classification and an iterative phylogenomic approach was used to reconstruct max_set and min_set FSF repertoires as upper and lower bounds of the urancestral proteome. While the functional make up of the urancestral sets was complex, they represent only 5-11% of the 1,420 FSFs of extant proteomes and their make up and reuse was at least 5 and 3 times smaller than proteomes of free-living organisms, repectively. Trees of proteomes reconstructed directly from FSFs or from molecular functions, which included the max_set and min_set as articial taxa, showed that urancestors were always placed at their base and rooted the tree of life in Archaea. Finally, a molecular clock of FSFs suggests the min_set reflects urancestral genetic make up more reliably and confirms diversified life emerged about 2.9 billion years ago during the start of planet oxygenation.ConclusionsThe minimum urancestral FSF set reveals the urancestor had advanced metabolic capabilities, was especially rich in nucleotide metabolism enzymes, had pathways for the biosynthesis of membrane sn1,2 glycerol ester and ether lipids, and had crucial elements of translation, including a primordial ribosome with protein synthesis capabilities. It lacked however fundamental functions, including transcription, processes for extracellular communication, and enzymes for deoxyribonucleotide synthesis. Proteomic history reveals the urancestor is closer to a simple progenote organism but harbors a rather complex set of modern molecular functions.

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Section: Discussionmentioning

confidence: 99%

The proteomic complexity and rise of the primordial ancestor of diversified life

2011

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“…Representatives of these EFLs and their evolutionary prototypes ( 20 , 21 ) can be found in different protein families, superfamilies and folds ( 27 ), allowing one to unravel deep evolutionary connections in the modern-day protein universe ( 2 ). These connections showed that the evolution of protein function ( 28 , 29 ) is complex, and, in addition to domain recombination, may have been driven by recombination of functional segments between protein domains ( 2 , 27 , 30 , 31 ). However, the specificity of molecular interactions in evolutionary conserved prototypes ( 20 ) and omnipresence of their descendants in protein folds and functions motivated us to develop a computational procedure for their derivation that differs from ancestral reconstruction due to the absence of any phylogenetic assumptions ( 20 , 21 ).…”

Section: Theoretical Background and Computational Methodsmentioning

confidence: 99%

Nucleotide binding database NBDB – a collection of sequence motifs with specific protein-ligand interactions

2015

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NBDB database describes protein motifs, elementary functional loops (EFLs) that are involved in binding of nucleotide-containing ligands and other biologically relevant cofactors/coenzymes, including ATP, AMP, ATP, GMP, GDP, GTP, CTP, PAP, PPS, FMN, FAD(H), NAD(H), NADP, cAMP, cGMP, c-di-AMP and c-di-GMP, ThPP, THD, F-420, ACO, CoA, PLP and SAM. The database is freely available online at http://nbdb.bii.a-star.edu.sg. In total, NBDB contains data on 249 motifs that work in interactions with 24 ligands. Sequence profiles of EFL motifs were derived de novo from nonredundant Uniprot proteome sequences. Conserved amino acid residues in the profiles interact specifically with distinct chemical parts of nucleotide-containing ligands, such as nitrogenous bases, phosphate groups, ribose, nicotinamide, and flavin moieties. Each EFL profile in the database is characterized by a pattern of corresponding ligand–protein interactions found in crystallized ligand–protein complexes. NBDB database helps to explore the determinants of nucleotide and cofactor binding in different protein folds and families. NBDB can also detect fragments that match to profiles of particular EFLs in the protein sequence provided by user. Comprehensive information on sequence, structures, and interactions of EFLs with ligands provides a foundation for experimental and computational efforts on design of required protein functions.

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“…The study revealed that structural elements involved in ribosomal mechanics were primordial. Subsequent studies generated detailed phylogenetic models of macromolecular accretion, confirmed that ribosomal structures supporting processive readings of RNA originated earlier than the peptidyl transferase center (PTC) responsible for protein synthesis, and revealed tight coevolution between rRNA and associated proteins of the universally conserved ribosomal core (Caetano-Anollés et al 2008 ; Sun and Caetano-Anollés 2009 ; Harish and Caetano-Anollés 2012 ). In contrast, a series of nomothetic studies simulated the evolution of the large subunit rRNA by dissecting helical-stack interactions in A-minor motifs and building up rRNA structures in concentric shells (e.g., Bokov and Steinberg 2009 ; Hsiao et al 2009 ).…”

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Ancestral Insertions and Expansions of rRNA do not Support an Origin of the Ribosome in Its Peptidyl Transferase Center

Caetano‐Anollés

2015

J Mol Evol

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Phylogenetic reconstruction of ribosomal history suggests that the ribonucleoprotein complex originated in structures supporting RNA decoding and ribosomal mechanics. A recent study of accretion of ancestral expansion segments of rRNA, however, contends that the large subunit of the ribosome originated in its peptidyl transferase center (PTC). Here I re-analyze the rRNA insertion data that supports this claim. Analysis of a crucial three-way junction connecting the long-helical coaxial branch that supports the PTC to the L1 stalk and its translocation functions reveals an incorrect branch-to-trunk insertion assignment that is in conflict with the PTC-centered accretion model. Instead, the insertion supports the ancestral origin of translocation. Similarly, an insertion linking a terminal coaxial trunk that holds the L7–12 stalk and its GTPase center to a seven-way junction of the molecule again questions the early origin of the PTC. Unwarranted assumptions, dismissals of conflicting data, structural insertion ambiguities, and lack of phylogenetic information compromise the construction of an unequivocal insertion-based model of macromolecular accretion. Results prompt integration of phylogenetic and structure-based models to address RNA junction growth and evolutionary constraints acting on ribosomal structure.Electronic supplementary materialThe online version of this article (doi:10.1007/s00239-015-9677-9) contains supplementary material, which is available to authorized users.

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Origins and evolution of modern biochemistry: insights from genomes and molecular structure

Cited by 17 publications

References 240 publications

The proteomic complexity and rise of the primordial ancestor of diversified life

The proteomic complexity and rise of the primordial ancestor of diversified life

Nucleotide binding database NBDB – a collection of sequence motifs with specific protein-ligand interactions

Ancestral Insertions and Expansions of rRNA do not Support an Origin of the Ribosome in Its Peptidyl Transferase Center

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